Input data and parameters
Input
Analysis date: | Sun Oct 29 13:07:22 GMT 2023 |
BAM file: | SRX7354151.markdup.sorted.bam |
Counting algorithm: | uniquely-mapped-reads |
GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf |
Number of bases for 5'-3' bias computation: | 100 |
Number of transcripts for 5'-3' bias computation: | 1,000 |
Paired-end sequencing: | yes |
Protocol: | strand-specific-reverse |
Sorting performed: | yes |
Summary
Reads alignment
Number of mapped reads (left/right): | 39,209,076 / 39,176,786 |
Number of aligned pairs (without duplicates): | 39,170,967 |
Total number of alignments: | 82,782,493 |
Number of secondary alignments: | 4,396,631 |
Number of non-unique alignments: | 7,375,215 |
Aligned to genes: | 64,308,824 |
Ambiguous alignments: | 220,081 |
No feature assigned: | 10,587,762 |
Missing chromosome in annotation: | 290,611 |
Not aligned: | 7,731,602 |
Reads genomic origin
Exonic: | 64,308,824 / 85.86% |
Intronic: | 7,313,756 / 9.77% |
Intergenic: | 3,274,006 / 4.37% |
Intronic/intergenic overlapping exon: | 2,881,661 / 3.85% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.2 |
5'-3' bias: | 1.82 |
Junction analysis
Reads at junctions: | 21,977,265 |
ACCT | 5.26% |
AGGT | 4.65% |
ATCT | 3.73% |
AGGA | 3.55% |
TCCT | 3.36% |
GCCT | 3.12% |
AGCT | 2.78% |
AGGC | 2.41% |
AGAT | 2.33% |
CCCT | 2.33% |
TTCT | 2.16% |